You can't re-order the display stack for rich media annotations (RMAs) - they will always appear on top. While it is possible to show and hide RMAs by promoting them to layers in the PDF via Preflight, in reality it doesn't work properly - it was never intended to be a supported configuration.
The correct way to do this is to include all your 3D models in the same scene, and show/hide them on a node-by-node basis using JavaScript attached to the RMA. See the Acrobat SDK for information.